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libsbml.SBMLErrorLog Class Reference
Inheritance diagram for libsbml.SBMLErrorLog:
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Detailed Description

{core}

Log of errors and other events encountered during SBML processing.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The error log is a list. Each SBMLDocument maintains its own SBMLErrorLog. When a libSBML operation on SBML content results in an error, or when there is something worth noting about the SBML content, the issue is reported as an SBMLError object stored in the SBMLErrorLog list.

SBMLErrorLog is derived from XMLErrorLog, an object class that serves exactly the same purpose but for the XML parsing layer. XMLErrorLog provides crucial methods such as getNumErrors() for determining how many SBMLError or XMLError objects are in the log. SBMLErrorLog inherits these methods.

The general approach to working with SBMLErrorLog in user programs involves first obtaining a pointer to a log from a libSBML object such as SBMLDocument. Callers should then use getNumErrors() to inquire how many objects there are in the list. (The answer may be 0.) If there is at least one SBMLError object in the SBMLErrorLog instance, callers can then iterate over the list using SBMLErrorLog.getError(), using methods provided by the SBMLError class to find out the error code and associated information such as the error severity, the message, and the line number in the input.

If you wish to simply print the error strings for a human to read, an easier and more direct way might be to use SBMLDocument.printErrors().

See also
SBMLError
XMLErrorLog
XMLError

Public Member Functions

def add
 
def changeErrorSeverity
 
def clearLog
 
def contains
 
def getError
 
def getNumErrors
 
def getNumFailsWithSeverity
 
def getSeverityOverride
 
def isSeverityOverridden
 
def printErrors
 
def remove
 
def setSeverityOverride
 
def toString
 
def unsetSeverityOverride
 

Member Function Documentation

def libsbml.SBMLErrorLog.add (   self,
  args 
)

Python method signature(s):

add(SBMLErrorLog self, SBMLError error)
def libsbml.XMLErrorLog.changeErrorSeverity (   self,
  args 
)
inherited

Python method signature(s):

changeErrorSeverity(XMLErrorLog self, long originalSeverity, long targetSeverity, string package="all")
changeErrorSeverity(XMLErrorLog self, long originalSeverity, long targetSeverity)

Changes the severity override for errors in the log that have a given severity.

This searches through the list of errors in the log, comparing each one's severity to the value of originalSeverity. For each error encountered with that severity logged by the named package, the severity of the error is reset to targetSeverity.

Parameters
originalSeveritythe severity code to match
targetSeveritythe severity code to use as the new severity
packagea string, the name of an SBML Level 3 package extension to use to narrow the search for errors. A value of 'all' signifies to match against errors logged from any package; a value of a package nickname such as 'comp' signifies to limit consideration to errors from just that package.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
See also
getSeverityOverride()
def libsbml.XMLErrorLog.clearLog (   self)
inherited

Python method signature(s):

clearLog(XMLErrorLog self)

Deletes all errors from this log.

def libsbml.SBMLErrorLog.contains (   self,
  args 
)

Python method signature(s):

contains(SBMLErrorLog self, long errorId)   bool

Returns true if SBMLErrorLog contains an errorId

Parameters
errorIdthe error identifier of the error to be found.
def libsbml.SBMLErrorLog.getError (   self,
  args 
)

{core}

Log of errors and other events encountered during SBML processing.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The error log is a list. Each SBMLDocument maintains its own SBMLErrorLog. When a libSBML operation on SBML content results in an error, or when there is something worth noting about the SBML content, the issue is reported as an SBMLError object stored in the SBMLErrorLog list.

SBMLErrorLog is derived from XMLErrorLog, an object class that serves exactly the same purpose but for the XML parsing layer. XMLErrorLog provides crucial methods such as getNumErrors() for determining how many SBMLError or XMLError objects are in the log. SBMLErrorLog inherits these methods.

The general approach to working with SBMLErrorLog in user programs involves first obtaining a pointer to a log from a libSBML object such as SBMLDocument. Callers should then use getNumErrors() to inquire how many objects there are in the list. (The answer may be 0.) If there is at least one SBMLError object in the SBMLErrorLog instance, callers can then iterate over the list using SBMLErrorLog.getError(), using methods provided by the SBMLError class to find out the error code and associated information such as the error severity, the message, and the line number in the input.

If you wish to simply print the error strings for a human to read, an easier and more direct way might be to use SBMLDocument.printErrors().

See also
SBMLError
XMLErrorLog
XMLError Python method signature(s):
getError(SBMLErrorLog self, long n)   SBMLError

Returns the nth SBMLError object in this log.

Index n is counted from 0. Callers should first inquire about the number of items in the log by using the getNumErrors() method. Attempts to use an error index number that exceeds the actual number of errors in the log will result in a None being returned.

Parameters
nthe index number of the error to retrieve (with 0 being the first error).
Returns
the nth SBMLError in this log, or None if n is greater than or equal to getNumErrors().
See also
getNumErrors()
def libsbml.XMLErrorLog.getNumErrors (   self)
inherited

{core}

Log of errors and other events encountered while processing an XML file or data stream.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The error log is a list. The XML layer of libSBML maintains an error log associated with a given XML document or data stream. When an operation results in an error, or when there is something wrong with the XML content, the problem is reported as an XMLError object stored in the XMLErrorLog list. Potential problems range from low-level issues (such as the inability to open a file) to XML syntax errors (such as mismatched tags or other problems).

A typical approach for using this error log is to first use getNumErrors() to inquire how many XMLError object instances it contains, and then to iterate over the list of objects one at a time using getError(long n) const. Indexing in the list begins at 0.

In normal circumstances, programs using libSBML will actually obtain an SBMLErrorLog rather than an XMLErrorLog. The former is subclassed from XMLErrorLog and simply wraps commands for working with SBMLError objects rather than the low-level XMLError objects. Classes such as SBMLDocument use the higher-level SBMLErrorLog. Python method signature(s):

getNumErrors(XMLErrorLog self)   long

Returns the number of errors that have been logged.

To retrieve individual errors from the log, callers may use XMLErrorLog.getError() .

Returns
the number of errors that have been logged.
def libsbml.SBMLErrorLog.getNumFailsWithSeverity (   self,
  args 
)

Python method signature(s):

getNumFailsWithSeverity(SBMLErrorLog self, long severity)   long
getNumFailsWithSeverity(SBMLErrorLog self, long severity)   long

Returns the number of errors that have been logged with the given severity code.

LibSBML associates severity levels with every SBMLError object to provide an indication of how serious the problem is. Severities range from informational diagnostics to fatal (irrecoverable) errors. Given an SBMLError object instance, a caller can interrogate it for its severity level using methods such as SBMLError.getSeverity(), SBMLError.isFatal(), and so on. The present method encapsulates iteration and interrogation of all objects in an SBMLErrorLog, making it easy to check for the presence of error objects with specific severity levels.
Parameters
severitya value from the set of LIBSBML_SEV_ constants defined by the interface class libsbml.
Returns
a count of the number of errors with the given severity code.
See also
getNumErrors()
def libsbml.XMLErrorLog.getSeverityOverride (   self)
inherited

Python method signature(s):

getSeverityOverride(XMLErrorLog self)   long

Returns the current override.

Returns
a severity override code. The possible values are:
See also
setSeverityOverride()
def libsbml.XMLErrorLog.isSeverityOverridden (   self)
inherited

Python method signature(s):

isSeverityOverridden(XMLErrorLog self)   bool

Returns a boolean indicating whether or not the severity has been overridden.

Returns
True if an error severity override has been set, False otherwise.
See also
setSeverityOverride()
def libsbml.XMLErrorLog.printErrors (   self,
  args 
)
inherited

Python method signature(s):

printErrors(XMLErrorLog self, ostream stream=cerr)
printErrors(XMLErrorLog self)

Prints all the errors or warnings stored in this error log.

This method prints the text to the stream given by the optional parameter stream. If no stream is given, the method prints the output to the standard error stream.

The format of the output is:

   N error(s):
     line NNN: (id) message

If no errors have occurred, i.e., getNumErrors() == 0, then no output will be produced.

Parameters
streamthe ostream or ostringstream object indicating where the output should be printed.
Documentation note:
The native C++ implementation of this method defines a default argument value. In the documentation generated for different libSBML language bindings, you may or may not see corresponding arguments in the method declarations. For example, in Java and C#, a default argument is handled by declaring two separate methods, with one of them having the argument and the other one lacking the argument. However, the libSBML documentation will be identical for both methods. Consequently, if you are reading this and do not see an argument even though one is described, please look for descriptions of other variants of this method near where this one appears in the documentation.
def libsbml.SBMLErrorLog.remove (   self,
  args 
)

Python method signature(s):

remove(SBMLErrorLog self, long errorId)

Removes an error having errorId from the SBMLError list.

Only the first item will be removed if there are multiple errors with the given errorId.

Parameters
errorIdthe error identifier of the error to be removed.
def libsbml.XMLErrorLog.setSeverityOverride (   self,
  args 
)
inherited

Python method signature(s):

setSeverityOverride(XMLErrorLog self, long severity)

Set the severity override.

Parameters
severityan override code indicating what to do. If the value is LIBSBML_OVERRIDE_DISABLED (the default setting) all errors logged will be given the severity specified in their usual definition. If the value is LIBSBML_OVERRIDE_WARNING, then all errors will be logged as warnings. If the value is LIBSBML_OVERRIDE_DONT_LOG, no error will be logged, regardless of their severity.
See also
getSeverityOverride()
def libsbml.XMLErrorLog.toString (   self)
inherited

Python method signature(s):

toString(XMLErrorLog self)   string

Writes all errors contained in this log to a string and returns it.

This method uses printErrors() to format the diagnostic messages. Please consult that method for information about the organization of the messages in the string returned by this method.

Returns
a string containing all logged errors and warnings.
See also
printErrors()
def libsbml.XMLErrorLog.unsetSeverityOverride (   self)
inherited

Python method signature(s):

unsetSeverityOverride(XMLErrorLog self)

Usets an existing override.

See also
setSeverityOverride()